medRxiv preprint doi: https://doi.org/10.1101/2020.05.21.20104521; this version posted May 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel Danielle Miller1*, Michael A. Martin2,3*, Noam Harel1*, Talia Kustin1*, Omer Tirosh1*, Moran Meir1, Nadav SoreK4, Shiraz Gefen-Halevi5, Sharon Amit5, Olesya Vorontsov6, Dana Wolf6, Avi Peretz7,8, Yonat Shemer-Avni9, Diana Roif-KaminsKy10, Na’ama Kopelman11, Amit Huppert12,13, Katia Koelle2, Adi Stern1,14 1 School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel 2 Department of Biology, Emory University, Atlanta, GA, USA 3 Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA 4 Microbiology laboratory, Assuta Ashdod University-Affiliated Hospital. Ashdod, Israel 5 Clinical Microbiology Laboratory, Sheba Medical Center, Ramat-Gan, Israel 6 Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel. 7 The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel 8 Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Poriya, Tiberias, Israel 9 Clinical Virology Laboratory, SoroKa Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel 10 Microbiology Division, Barzilai University Medical Center, AshKelon, Israel 11 Department of Computer Science, Holon Institute of Technology, Holon, Israel 12 Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology and, Health Policy Research, Chaim Sheba Medical Center, Tel Hashomer, 52621 Israel 13 School of Public Health, the SacKler Faculty of Medicine, Tel-Aviv University, Tel Aviv, 69978 Israel 14 Edmond J. Safra Center for Bioinformatics at Tel Aviv University * Co-equal authorship ABSTRACT Full genome sequences are increasingly used to tracK the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequenced 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. A phylogenetic analysis including thousands of globally sampled sequences allowed us to infer multiple independent introductions into Israel, followed by local transmission. Returning travelers from the U.S. contributed dramatically more to viral spread relative to their proportion in incoming infected travelers. Using phylodynamic analysis, we estimated that the basic reproduction number of the virus was initially around ~2.0-2.6, dropping by two-thirds following the implementation of social distancing measures. A comparison between reported and model-estimated case numbers indicated high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 1-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings underscore the ability of this virus to efficiently transmit between and within countries, as well as demonstrate the effectiveness of social distancing measures for reducing its spread. NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. 1 medRxiv preprint doi: https://doi.org/10.1101/2020.05.21.20104521; this version posted May 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . INTRODUCTION In December 2019 an outbreaK of severe respiratory disease was identified in Wuhan, China (Huang, et al. 2020). Shortly later, the etiological agent of the disease was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Zhou, et al. 2020; Zhu, et al. 2020), and the disease caused by the virus was named coronavirus disease 19 (COVID-19). The virus has since spread rapidly across the globe, causing a WHO-declared pandemic with social and economic devastation in many regions of the world. The infectious disease research community has quicKly stepped up to the tasK of characterizing the virus and its replication dynamics, describing its pathogenesis, and tracKing its movement through the human population. Parameterized epidemiological models have been particularly informative of how this virus has spread with and without control measures in place (e.g., Tian, et al. 2020), and have been used to project viral spread both in the short-term (Flaxman, et al. 2020) and in the more distant future (Kissler, et al. 2020). Along with epidemiological analysis based on case reports and COVID-19 death data, sequencing of viral genomes has become a powerful tool in understanding and tracKing the dynamics of infections (Volz, et al. 2013; Gardy and Loman 2018). So-called “genomic epidemiology” allows for effective reconstruction of viral geographical spread as well as estimation of Key epidemiological quantities such as the basic reproduction number of a virus, its growth rate and doubling time, and patterns of disease incidence and prevalence. Such insights have been used to inform policy maKers during various pathogen outbreaKs, as occurred for example in the 2014-2016 outbreaK of Ebola virus in West Africa (Khoury, et al. 2018; Armstrong, et al. 2019), and during this current SARS-CoV-2 pandemic (Bedford, et al. 2020; Fauver, et al. 2020). Here, we set out to sequence SARS-CoV-2 from samples across the state of Israel, with the aim of gaining a better understanding of introductions of the virus into Israel, spread of the virus inside the country, and the epidemiology of the disease, including (a) the basic reproduction number of the virus before and after social distancing measures were implemented, and (b) the extent of viral superspreading within Israel. We sought to gain this understanding within the context of existing epidemiological Knowledge, including that the first confirmed cases of SARS-CoV-2 infection in Israel were reported in early-February, followed by many identified SARS-CoV-2 cases in travelers returning to Israel mainly from Europe and the United States. Growth in the number of verified cases rapidly ensued, which led to increased measures of social distancing, including the cessation of passenger flights to Israel, school closure, and eventually a near complete locKdown across the entire state of Israel. Quarantining of returning travelers from Europe was implemented between February 26 and March 4, 2020, and subsequently all incoming travel to Israel was arrested on March 9. In the meantime, the rate of testing was ramped up, eventually reaching a rate of more than 1,500 tests per million people per day. The reported daily incidence and reported numbers of daily severe cases peaKed around mid-April and have dropped steadily since then. Despite this Knowledge, many questions remain: Which of the multiple SARS-CoV-2 introductions resulted in sustained local transmission? How did the virus spread across the state? What was the magnitude of the virus’s reproduction potential within Israel, and to what extent did control measures mitigate its spread? Here, through a comprehensive set of phylogenetic and phylodynamic analyses, we quantitatively address these questions. 2 medRxiv preprint doi: https://doi.org/10.1101/2020.05.21.20104521; this version posted May 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . RESULTS & DISCUSSION In order to gain a better understanding of the dynamics of SARS-CoV-2 spread into and within Israel, we sequenced the virus from a cohort of patients representing a random sample across Israel, resulting in 212 full-genome SARS-CoV-2 sequences (Methods). A total of 224 unique single nucleotide variants (SNVs) were identified between the Wuhan reference sequence and this set of sequences from Israel. Figure 1 shows the distribution of identified SNVs along the genome and their counts in the sequenced samples. Of these SNVs, 141 were non-synonymous, 72 were synonymous, and the remaining 11 were in non- coding regions. One of the most abundantly detected SNVs was a non-synonymous variant D614G found in the spiKe protein, which was present in 90% of the sequences. This variant has generated much interest as it has been reported to potentially increase the transmissibility of the virus (Korber, et al. 2020). Of note however, the alternative hypothesis that the observed increases in this variant’s frequency is due to demographic considerations and genetic drift has not been ruled out. Figure 1. Variation found in sequenced samples from Israel. Counts of identified SNVs across the SARS-CoV-2 genome. We also found five different high confidence genomic deletions, spanning between one and eighteen nucleotides (Fig. 2) (Methods), each of which was found in one to two samples. Three of these five deletions occurred in multiples of three and were in-frame deletions or affected non-coding regions. Of the remaining two deletions, deletion #3 spanned ten nucleotides, and liKely prevents the translation of ORF7a. Deletion #4 occurred at the end of ORF8 and causes the replacement of the last amino acid with an additional five amino acids. Notably, an 81 nt in-frame deletion in ORF7a has been previously reported (Holland, et al. 2020), as has been a 382 nt deletion in ORF8 (Su, et al. 2020), suggesting that the virus is to some extent tolerant to deletions in these ORFs. 3 medRxiv preprint doi: https://doi.org/10.1101/2020.05.21.20104521; this version posted May 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.